With increasing reports of new, more dangerous COVID-19 variants in Ontario, experts say the province urgently needs more genomic sequencing, faster results, and policies that stifle the virus’s opportunities to evolve — a situation reminiscent of the earliest days of the pandemic, when the disease outstripped our ability to track and control it.
The province has ramped up surveillance for three red-flag “variants of concern,” which were first detected in the U.K., South Africa and Brazil. Unlike the many viral strains with mostly benign genetic alterations, these three variants carry a host of mutations that scientists believe makes them significantly more contagious or potentially able to evade some immune defences in previously infected and vaccinated people.
This past week, the Simcoe Muskoka public health unit announced that six samples from a vicious outbreak at the Roberta Place nursing home in Barrie had preliminarily screened positive for one of those variants. On Saturday, the health unit said that full genome sequencing confirmed the presence of the U.K. variant in all six. Twenty-nine residents have died after 124 of 127 tested positive for COVID-19 in less than two weeks, along with 84 staff and two visitors.
Public Health Ontario has asked every lab in the provincial COVID-19 testing network to forward all positive samples from Wednesday to be analyzed for the variants of concern — a single-day snapshot of about 2,630 cases. Initial results will be available in two to three weeks, according to Dr. Vanessa Allen, PHO’s chief of microbiology and laboratory science.
Outside of that “point-prevalence” study, the agency is conducting full sequencing on about 350 samples a week, and is poised to triple its capacity to carry out preliminary screening tests. Hospital and university labs are boosting those volumes, including a next-generation, ultra-high-throughput sequencing platform that will soon begin screening hundreds of samples from Toronto daily.
But experts say further investment is needed — financial and logistical — to make sure officials can catch and act on new information in time.
“This feels like February-March 2020 in some ways,” says Dr. Samira Mubareka, a microbiologist at Sunnybrook Health Sciences Centre, who has been involved in sequencing viral genomes from the beginning of the pandemic.
Canada is sequencing about five per cent of positive COVID-19 samples to hunt for variants, Mubareka says, about half of what the U.K. is achieving.
“At five per cent, you would have to have quite a few variants floating around to pick one up. And then you realize, well, it’s just the tip of the iceberg. By then you’re already in a bit of trouble.”
Developing fast, cheap screening tests for variants — ones that give a preliminary yes-or-no answer — is underway, experts say. By this week, PHO will be able to screen up to 1,500 weekly samples, according to a spokesperson. (With the six Roberta Place samples, Ontario has caught 21 confirmed cases of the U.K. variant and none of either the South African or Brazilian ones out of 4,000 tests since September.
But fully sequencing viral genomes — getting every word on every page of the genetic instruction manual, not just a yes-or-no — is critical to understanding exactly what strains are circulating, including not-yet-identified or even home-grown variants, a realistic threat at this stage of the pandemic.
Turnaround times for full genome sequences need to improve from the current two to three weeks, Mubareka says, pointing to the Roberta Place outbreak: public health needs actionable information, not a weeks-old snapshot.
Expanding the province’s genomic surveillance capacity involves more than just buying sequencing instruments, Mubareka says. Similar to the bottlenecks that have stymied conventional COVID-19 testing, it also requires ensuring that information flows quickly through the system — including supporting public health to carry out the same functions that have been vital since the very first case.
“There’s no point in generating this data if there aren’t those key track-and-trace teams on the other side to say, ‘OK, we’ve got this, we’re on it,’ and can actually intervene in an impactful way.”
At Sinai Health’s Lunenfeld-Tanenbaum Research Institute, scientists are working to adapt a next-generation, ultra-high-throughput sequencing platform to screen hundreds of positive samples for variants daily.
The platform is designed to sequence small genome sections very quickly and in huge volumes. Pre-pandemic, the scientists were using it to study cancer. This year, they worked to convert it into a system that could process thousands of conventional COVID-19 tests, research that is still advancing.
In December, researchers in the U.K. announced that a viral strain carrying a host of mutations was spreading rapidly, and appeared to be roughly 50 per cent more transmissible. The Sinai team pivoted again, adapting the platform to process hundreds of lab samples that already tested positive by rapidly sequencing “fingerprint regions” of the viral genome to look for key mutations.
“Three weeks later, (the information is) not as helpful, says Jeff Wrana, a senior investigator at LTRI who is leading the project. “We need to get it within days.”
The team recently carried out a proof-of-concept experiment, analyzing 900 positive COVID test samples from Sinai’s lab. They hope to start screening every positive sample from Sinai soon — around 400 a day.
Nearly all screening results from the pilot run were unremarkable, long-circulating strains of the virus, Wrana says.
Loading…
Loading…Loading…Loading…Loading…Loading…
According to genetic sequences uploaded to GISAID, an open-access database that researchers use to share, track and compare SARS-CoV-2 lineages, the team also found a small number of a viral variant from Brazil. This lineage, known as P.2, is not the same as the Brazilian variant of concern, which has not been detected in Ontario.
“We’re keeping an eye on it, because it could pick up more mutations and become a variant of concern. But at this point it’s just something we’re tracking and keeping an eye on. We’re not particularly concerned about it,” says Andrew McArthur, a professor and bioinformatics specialist at McMaster University’s Michael G. DeGroote Institute for Infectious Disease Research.
McArthur and Mubareka belong to the Toronto Invasive Bacterial Diseases Network, which in December and January also identified a small number of P.2 strains in Ontario, according to GISAID.
P.2 does not carry the spike protein mutation known as N501Y that is shared by all three red-flag variants, associated with significantly increased transmissibility. Aside from N501Y, the three variants of concern boast a large number of mutations in key regions, and scientists are working furiously to understand their combined effects.
RELATED STORIES
The strain Wrana and others identified in Toronto, however, does have a mutation known as E484K, which both the South African and Brazilian variants of concern share. Scientists are worried about variants carrying E484K, because laboratory experiments, case reports of reinfection and epidemiological evidence from South Africa and Brazil suggest the mutation helps evade immune response in people who have already been infected or vaccinated.
The real-world impacts of this are unclear, and even less clear in strains like P.2 that carry one “watchlist” mutation but not the full suite of worrying changes. Our immune systems have an armada of cellular defences, and weakening one part of the system doesn’t neutralize all of it. The Pfizer and Moderna vaccines in particular are so effective that losing some efficacy may not matter, and they can also be retooled quickly if necessary.
PHO’s Allen says that until the significance of key mutations are better known, the agency and local health units are carrying out additional case investigation for samples with strains carrying mutations like E484K as well as for the official variants of concern.
But that uncertainty is also why we need to remain vigilant — especially right now, scientists say.
“Never underestimate a virus or the cleverness of evolution. These variants are popping up all over,” Wrana says. “They should be aggressively monitored and controlled, because if they do have significant immune evasion properties, it would be devastating.”
Mubareka and McArthur both noted that public health policies and personal behaviour also have a significant effect on the evolution of new variants: every time the virus is transmitted, it has a chance to evolve.
“This is one of the most dangerous parts of the pandemic. Generating new variants is about time and number of patients, and we’ve had a lot of both,” says McArthur.
“The simplest way to reduce the risk of new variants is to drive the numbers down. It’s as simple as that.”
Kate Allen is a Toronto-based reporter covering science and technology for the Star. Follow her on Twitter: @katecallen
NAIROBI, Kenya (AP) — The body of Ugandan Olympic athlete Rebecca Cheptegei — who died after being set on fire by her partner in Kenya — was received Friday by family and anti-femicide crusaders, ahead of her burial a day later.
Cheptegei’s family met with dozens of activists Friday who had marched to the Moi Teaching and Referral Hospital’s morgue in the western city of Eldoret while chanting anti-femicide slogans.
She is the fourth female athlete to have been killed by her partner in Kenya in yet another case of gender-based violence in recent years.
Viola Cheptoo, the founder of Tirop Angels – an organization that was formed in honor of athlete Agnes Tirop, who was stabbed to death in 2021, said stakeholders need to ensure this is the last death of an athlete due to gender-based violence.
“We are here to say that enough is enough, we are tired of burying our sisters due to GBV,” she said.
It was a somber mood at the morgue as athletes and family members viewed Cheptegei’s body which sustained 80% of burns after she was doused with gasoline by her partner Dickson Ndiema. Ndiema sustained 30% burns on his body and later succumbed.
Ndiema and Cheptegei were said to have quarreled over a piece of land that the athlete bought in Kenya, according to a report filed by the local chief.
Cheptegei competed in the women’s marathon at the Paris Olympics less than a month before the attack. She finished in 44th place.
Cheptegei’s father, Joseph, said that the body will make a brief stop at their home in the Endebess area before proceeding to Bukwo in eastern Uganda for a night vigil and burial on Saturday.
“We are in the final part of giving my daughter the last respect,” a visibly distraught Joseph said.
He told reporters last week that Ndiema was stalking and threatening Cheptegei and the family had informed police.
Four in 10 women or an estimated 41% of dating or married Kenyan women have experienced physical or sexual violence perpetrated by their current or most recent partner, according to the Kenya Demographic and Health Survey 2022.
TEL AVIV, Israel (AP) — A rare Bronze-Era jar accidentally smashed by a 4-year-old visiting a museum was back on display Wednesday after restoration experts were able to carefully piece the artifact back together.
Last month, a family from northern Israel was visiting the museum when their youngest son tipped over the jar, which smashed into pieces.
Alex Geller, the boy’s father, said his son — the youngest of three — is exceptionally curious, and that the moment he heard the crash, “please let that not be my child” was the first thought that raced through his head.
The jar has been on display at the Hecht Museum in Haifa for 35 years. It was one of the only containers of its size and from that period still complete when it was discovered.
The Bronze Age jar is one of many artifacts exhibited out in the open, part of the Hecht Museum’s vision of letting visitors explore history without glass barriers, said Inbal Rivlin, the director of the museum, which is associated with Haifa University in northern Israel.
It was likely used to hold wine or oil, and dates back to between 2200 and 1500 B.C.
Rivlin and the museum decided to turn the moment, which captured international attention, into a teaching moment, inviting the Geller family back for a special visit and hands-on activity to illustrate the restoration process.
Rivlin added that the incident provided a welcome distraction from the ongoing war in Gaza. “Well, he’s just a kid. So I think that somehow it touches the heart of the people in Israel and around the world,“ said Rivlin.
Roee Shafir, a restoration expert at the museum, said the repairs would be fairly simple, as the pieces were from a single, complete jar. Archaeologists often face the more daunting task of sifting through piles of shards from multiple objects and trying to piece them together.
Experts used 3D technology, hi-resolution videos, and special glue to painstakingly reconstruct the large jar.
Less than two weeks after it broke, the jar went back on display at the museum. The gluing process left small hairline cracks, and a few pieces are missing, but the jar’s impressive size remains.
The only noticeable difference in the exhibit was a new sign reading “please don’t touch.”
VICTORIA – The British Columbia government is partnering with a bear welfare group to reduce the number of bears being euthanized in the province.
Nicholas Scapillati, executive director of Grizzly Bear Foundation, said Monday that it comes after months-long discussions with the province on how to protect bears, with the goal to give the animals a “better and second chance at life in the wild.”
Scapillati said what’s exciting about the project is that the government is open to working with outside experts and the public.
“So, they’ll be working through Indigenous knowledge and scientific understanding, bringing in the latest techniques and training expertise from leading experts,” he said in an interview.
B.C. government data show conservation officers destroyed 603 black bears and 23 grizzly bears in 2023, while 154 black bears were killed by officers in the first six months of this year.
Scapillati said the group will publish a report with recommendations by next spring, while an independent oversight committee will be set up to review all bear encounters with conservation officers to provide advice to the government.
Environment Minister George Heyman said in a statement that they are looking for new ways to ensure conservation officers “have the trust of the communities they serve,” and the panel will make recommendations to enhance officer training and improve policies.
Lesley Fox, with the wildlife protection group The Fur-Bearers, said they’ve been calling for such a committee for decades.
“This move demonstrates the government is listening,” said Fox. “I suspect, because of the impending election, their listening skills are potentially a little sharper than they normally are.”
Fox said the partnership came from “a place of long frustration” as provincial conservation officers kill more than 500 black bears every year on average, and the public is “no longer tolerating this kind of approach.”
“I think that the conservation officer service and the B.C. government are aware they need to change, and certainly the public has been asking for it,” said Fox.
Fox said there’s a lot of optimism about the new partnership, but, as with any government, there will likely be a lot of red tape to get through.
“I think speed is going to be important, whether or not the committee has the ability to make change and make change relatively quickly without having to study an issue to death, ” said Fox.
This report by The Canadian Press was first published Sept. 9, 2024.
